X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FDBRefEntry.java;h=ec6dcf8d76a0b83a986fc00a74b3b59d8ada17bc;hb=460c037bef9ec113c2a46010c443d85e73347592;hp=6a48da7597e4ecd1556308483b7e569ab1e6cf6e;hpb=168ef5a045478ef56a5d9f8c71fbddb53a6b8a58;p=jalview.git

diff --git a/src/jalview/datamodel/DBRefEntry.java b/src/jalview/datamodel/DBRefEntry.java
index 6a48da7..ec6dcf8 100755
--- a/src/jalview/datamodel/DBRefEntry.java
+++ b/src/jalview/datamodel/DBRefEntry.java
@@ -23,10 +23,12 @@ package jalview.datamodel;
 import jalview.api.DBRefEntryI;
 
 import java.util.Arrays;
+import java.util.List;
 
 public class DBRefEntry implements DBRefEntryI
 {
   String source = "", version = "", accessionId = "";
+
   /**
    * maps from associated sequence to the database sequence's coordinate system
    */
@@ -37,7 +39,6 @@ public class DBRefEntry implements DBRefEntryI
 
   }
 
-
   public DBRefEntry(String source, String version, String accessionId)
   {
     this(source, version, accessionId, null);
@@ -140,7 +141,8 @@ public class DBRefEntry implements DBRefEntryI
     String otherAccession = other.getAccessionId();
     if ((accessionId == null && otherAccession != null)
             || (accessionId != null && otherAccession == null)
-            || (accessionId != null && !accessionId.equalsIgnoreCase(otherAccession)))
+            || (accessionId != null && !accessionId
+                    .equalsIgnoreCase(otherAccession)))
     {
       return false;
     }
@@ -150,7 +152,7 @@ public class DBRefEntry implements DBRefEntryI
      * otherwise the versions have to match
      */
     String otherVersion = other.getVersion();
-      
+
     if ((version == null || version.equals("0") || version.endsWith(":0"))
             && otherVersion != null)
     {
@@ -225,28 +227,24 @@ public class DBRefEntry implements DBRefEntryI
     return accessionId;
   }
 
-
   @Override
   public void setAccessionId(String accessionId)
   {
     this.accessionId = accessionId;
   }
 
-
   @Override
   public void setSource(String source)
   {
     this.source = source;
   }
 
-
   @Override
   public void setVersion(String version)
   {
     this.version = version;
   }
 
-
   @Override
   public Mapping getMap()
   {
@@ -281,9 +279,10 @@ public class DBRefEntry implements DBRefEntryI
   public String toString()
   {
     return getSrcAccString();
+  }
 
   @Override
-  public boolean isPrimary()
+  public boolean isPrimaryCandidate()
   {
     /*
      * if a map is present, unless it is 1:1 and has no SequenceI mate, it cannot be a primary reference.  
@@ -299,6 +298,18 @@ public class DBRefEntry implements DBRefEntryI
       {
         return false;
       }
+      // check map is between identical single contiguous ranges
+      List<int[]> fromRanges = map.getMap().getFromRanges();
+      List<int[]> toRanges = map.getMap().getToRanges();
+      if (fromRanges.size() != 1 || toRanges.size() != 1)
+      {
+        return false;
+      }
+      if (fromRanges.get(0)[0] != toRanges.get(0)[0]
+              || fromRanges.get(0)[1] != toRanges.get(0)[1])
+      {
+        return false;
+      }
     }
     if (version == null)
     {
@@ -321,5 +332,4 @@ public class DBRefEntry implements DBRefEntryI
     }
     return true;
   }
-  }
 }